OK. When I delete software in the CMS section it shows up at the bottom of the section and is unchecked. It was checked and restored.

I am wondering though about upgrading specific software. I assume that if I have a Joomla 1.71 install and you upgrade to 2.0 it will not alter the already installed version and I can continue using that version. The only issue is if I need to reinstall and will no longer have that version.

Sir you can enable the script by simply going to Softaculous Admin Panel -> Software selecting the checkbox of your desired script and click on Update Settings. This will enable the script for installation.

We support the latest stable versions of scripts. For Joomla we support two branches i.e. 1.5.25 and 1.7.3